The development of biomolecular control systems that can be deployed in vivo is critical to harnessing cells for future biotechnology, energy, and medical applications. We engineer RNA networks that enable living cells to detect intracellular RNA molecules and perform computations. These RNA-based computing systems make use of de novo RNA sequence design and the predictable base pairing properties of RNA to control cellular behavior. These capabilities are enabled using RNA-based regulators, or riboregulators, that have the capacity to bind to target transcripts in the cell to modulate gene expression.

The video below shows how one of our riboregulators called a toehold switch works. Toehold switches are engineered for use in prokaryotic cells and have the ability to activate translation in response to nearly any RNA target sequence. More recently, we have developed riboregulators that can turn off translation when they bind to a target RNA and others can specifically detect RNAs with single-nucleotide mutations.

After we identify riboregulators with good performance and that operate independently, we can use them as modular parts in RNA-based circuits for biological computing. These circuits can respond to as many as a dozen different RNA species and have the potential to interface directly with the native transcriptome for biosensing applications. 

  1. A. A. Green, P. A. Silver, J. J. Collins & P. Yin, “Toehold Switches: De-Novo-Designed Regulators of Gene Expression,” Cell 159, 925-939 (2014).
  2. A. A. Green*,†, J. Kim*, D. Ma, P. A. Silver, J. J. Collins & P. Yin, “Complex cellular logic computation using ribocomputing devices,” Nature 548, 117-121 (2017).
  3. J. Kim, P. Yin & A. A. Green, “Ribocomputing: Cellular Logic Computation Using RNA Devices,” Biochemistry 57, 883-885 (2017).
  4. J. Li, A. A. Green, H. Yan & C. Fan, “DNA nanotechnology for programmable molecular circuitry and intracellular biocomputation,” Nature Chemistry 9, 1056-1067 (2017).
  5. J. Kim*, Y. Zhou*, P. Carlson, M. Teichmann, F. C. Simmel, P. A. Silver, J. J. Collins, J. B. Lucks, P. Yin & A. A. Green, “De-Novo-Designed Translation-Repressing Riboregulators for Multi-Input Cellular Logic,” Nature Chemical Biology published online (2019) bioRxiv.